Contacts of the helix formed by residues 229 - 249 (chain A) in PDB entry 2AXV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.5 26.7 - - + +
191A GLN* 2.9 23.1 + - - +
227A SER 3.4 3.2 + - - -
228A ILE* 1.3 76.4 - - - +
230A GLY* 1.3 58.4 + - - +
231A TYR* 2.8 31.3 + - - +
232A TYR* 3.3 29.6 + - + +
233A ASP 2.8 22.5 + - - -
228B ILE 5.4 1.7 - - - +
230B GLY 5.1 0.9 + - - -
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Residues in contact with GLY 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ILE 3.3 5.7 + - - -
229A ASN* 1.3 70.3 + - - +
231A TYR* 1.3 61.0 + - - +
233A ASP* 3.7 1.4 - - - +
234A LEU* 3.0 31.5 + - - +
229B ASN* 5.0 0.6 + - - -
230B GLY* 4.2 10.8 - - - +
231B TYR* 3.5 45.0 - - - -
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Residues in contact with TYR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASN* 2.8 20.2 + - - +
230A GLY* 1.3 71.9 - - - +
232A TYR* 1.3 68.5 + - + +
234A LEU* 3.4 11.2 + - + +
235A GLU* 3.0 25.4 + - - +
264A PHE* 3.6 14.3 - + + -
267A ILE* 4.0 10.5 - - + -
269A LYS* 3.1 44.9 + - + +
272A ILE* 4.4 13.7 - - + -
221B LYS* 5.3 0.3 - - - -
228B ILE* 3.3 45.4 - - + +
230B GLY* 3.8 19.0 - - - -
233B ASP* 2.8 25.3 + - - -
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.3 26.9 - - + +
191A GLN* 3.4 30.1 - - + +
192A THR* 2.8 43.1 + - - +
195A LYS* 3.3 36.1 + - + -
217A PHE* 4.3 9.4 - + + -
229A ASN* 3.3 26.1 + - + +
231A TYR* 1.3 80.1 - - + +
233A ASP* 1.3 63.9 + - - +
235A GLU* 3.1 6.4 + - - +
236A ILE* 2.8 34.0 + - + +
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Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PHE* 3.8 10.5 - - - -
221A LYS* 2.9 36.2 + - - +
228A ILE* 4.1 2.7 - - + -
229A ASN 2.8 12.6 + - - +
230A GLY 3.2 4.4 + - - +
232A TYR* 1.3 70.9 - - - +
234A LEU* 1.3 57.1 + - - +
236A ILE* 3.9 0.9 - - - +
237A ASN* 2.9 46.6 + - - +
231B TYR* 2.8 44.9 + - + +
267B ILE* 3.7 17.6 - - + +
269B LYS* 4.1 6.4 - - - +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY 3.0 14.1 + - - +
231A TYR* 3.4 12.8 - - + +
233A ASP* 1.3 78.6 - - - +
235A GLU* 1.3 57.9 + - - +
237A ASN* 3.1 6.6 + - - +
238A TYR 2.9 22.9 + - - -
260A ILE* 3.7 32.0 - - + +
263A ILE* 4.2 14.4 - - + -
264A PHE* 3.5 23.8 - - + -
267A ILE* 5.0 7.2 - - + -
230B GLY 5.7 3.4 - - - +
234B LEU* 4.2 22.4 - - + -
263B ILE* 3.8 27.4 - - + -
267B ILE* 4.2 16.8 - - + +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 3.1 42.4 + - + +
199A THR* 4.7 4.9 + - - +
231A TYR 3.0 14.0 + - - +
232A TYR* 3.1 5.8 + - - +
234A LEU* 1.3 75.2 - - - +
236A ILE* 1.3 66.8 + - - +
237A ASN 3.1 1.1 - - - -
238A TYR* 3.2 17.2 + - + +
239A LEU* 3.0 24.5 + - + +
264A PHE* 4.0 7.0 - - + -
272A ILE* 3.4 31.2 - - + +
276A LEU* 3.9 28.6 - - + +
279A GLU* 5.5 1.2 - - - +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLN 5.1 0.2 - - - +
194A LEU 4.7 1.6 - - - -
195A LYS* 3.9 40.8 - - + +
198A LEU* 3.8 20.5 - - + +
214A ILE* 5.3 4.9 - - + -
217A PHE* 3.4 60.8 - - + -
218A GLU* 5.3 4.7 - - - +
232A TYR* 2.8 16.4 + - + +
233A ASP 4.1 1.6 - - - +
235A GLU* 1.3 77.1 - - - +
237A ASN* 1.3 60.2 + - - +
239A LEU* 3.0 9.9 + - + +
240A LYS* 2.9 29.9 + - + +
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Residues in contact with ASN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLU* 4.9 1.0 + - - -
221A LYS* 4.2 6.5 - - - +
233A ASP* 2.9 41.3 + - - +
234A LEU 3.1 5.6 + - - +
236A ILE* 1.3 78.2 - - - +
238A TYR* 1.3 64.4 + - - +
240A LYS* 3.3 30.2 + - - +
241A GLN* 3.0 31.9 + - - +
260A ILE* 3.9 4.9 - - + -
266B ILE* 3.5 19.4 - - - +
267B ILE* 3.5 36.5 + - + +
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU 2.9 11.9 + - - +
235A GLU* 3.3 15.7 - - + +
237A ASN* 1.3 78.0 - - - +
239A LEU* 1.3 76.0 + - + +
241A GLN* 3.1 6.2 - - - +
242A ILE* 3.1 42.3 + - + +
257A ALA* 3.6 21.3 - - + -
260A ILE* 3.6 24.4 - - + +
261A ILE* 3.3 27.8 - - + -
276A LEU* 3.7 26.4 + - + -
279A GLU* 3.3 40.8 + - - +
280A LEU* 3.8 5.6 + - + -
283A ILE* 3.9 9.5 - - - +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 4.3 4.3 - - + +
198A LEU* 3.5 40.8 - - + -
199A THR* 3.9 24.7 - - + +
202A ILE* 3.8 28.4 - - + +
214A ILE* 5.2 0.2 - - - -
235A GLU* 3.0 23.5 + - + +
236A ILE* 3.0 13.2 + - + +
238A TYR* 1.3 94.9 - - + +
240A LYS* 1.3 59.9 + - - +
241A GLN 3.0 1.6 - - - -
242A ILE* 3.2 5.8 + - + +
243A TYR* 2.8 29.2 + - - +
279A GLU* 4.1 9.6 - - - +
283A ILE* 6.0 0.2 - - + -
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 3.6 38.2 - - + +
218A GLU* 3.0 30.7 + - - +
236A ILE* 2.9 14.8 + - + +
237A ASN* 3.3 30.4 + - - +
239A LEU* 1.3 75.6 - - - +
241A GLN* 1.3 60.1 + - - +
243A TYR* 3.3 9.1 + - + +
244A GLN* 3.0 52.9 + - - +
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ASN* 3.0 20.4 + - - +
238A TYR* 3.1 17.7 - - - +
240A LYS* 1.3 78.2 - - - +
242A ILE* 1.3 61.2 - - - +
243A TYR 3.4 0.2 + - - -
244A GLN* 3.3 25.0 + - - +
245A PHE* 3.2 15.9 + - - +
253A SER* 3.3 32.9 + - - +
256A ASN* 2.9 51.2 + - + +
257A ALA* 3.5 7.6 - - + +
260A ILE* 4.7 2.9 - - + +
266B ILE* 4.2 18.2 + - - +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 4.1 13.9 - - + -
238A TYR* 3.1 34.6 + - + +
239A LEU* 3.2 7.6 + - - +
241A GLN* 1.3 75.1 - - - +
243A TYR* 1.3 57.8 + - - +
245A PHE* 3.1 9.1 + - + +
246A LEU* 2.9 37.6 + - + +
254A TYR* 5.2 9.2 - - + -
257A ALA* 3.4 24.5 - - + -
280A LEU* 3.8 25.6 - - + -
283A ILE* 4.0 28.5 - - + -
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Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 4.0 11.8 - - + +
207A LEU* 3.3 41.1 + - + +
210A ALA* 4.0 16.4 - - + -
211A GLN* 3.3 36.8 + - + +
214A ILE* 4.1 13.7 - - + -
239A LEU 2.8 16.8 + - - +
240A LYS* 3.4 13.0 - - + +
241A GLN 3.2 0.2 - - - -
242A ILE* 1.3 77.6 - - - +
244A GLN* 1.3 69.8 + - + +
246A LEU* 3.1 7.4 + - - +
247A THR* 2.8 48.1 + - + +
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Residues in contact with GLN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LYS* 3.0 39.2 + - - +
241A GLN* 3.3 24.2 + - - +
242A ILE 3.3 0.2 - - - -
243A TYR* 1.3 85.3 - - + +
245A PHE* 1.3 57.5 + - - +
247A THR* 3.1 9.8 + - - +
248A ASP* 3.1 21.6 + - - +
250A ASN* 3.0 22.2 + - - +
253A SER* 3.3 13.7 + - - +
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLN 3.2 11.5 + - - +
242A ILE* 3.1 15.6 + - + +
243A TYR 3.1 0.8 - - - -
244A GLN* 1.3 76.2 - - - +
246A LEU* 1.3 70.3 + - + +
249A LYS* 2.8 53.5 + - + +
250A ASN 3.1 44.9 - - - +
251A ILE* 4.5 2.7 - - - -
253A SER* 3.8 8.2 - - - -
254A TYR* 3.9 36.6 - + + +
283A ILE* 6.1 1.1 - - + -
287A GLU* 4.5 14.4 - - + -
289A PHE* 3.7 33.7 - + - -
289C PHE* 4.8 5.6 - + - -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 4.4 15.7 - - + +
205A ARG* 3.4 37.5 + - + +
207A LEU* 4.0 26.7 - - + +
242A ILE* 2.9 34.9 + - + +
243A TYR* 3.1 7.8 + - - +
245A PHE* 1.3 80.7 - - + +
247A THR* 1.3 63.8 + - - +
249A LYS* 4.3 5.4 + - - +
283A ILE* 4.1 13.0 - - + -
287A GLU* 3.1 43.5 - - + +
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Residues in contact with THR 247 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A LEU* 3.6 24.7 - - + -
243A TYR* 2.8 48.4 + - + +
244A GLN* 3.1 15.8 + - - +
246A LEU* 1.3 79.4 - - - +
248A ASP* 1.3 73.0 + - - +
249A LYS 3.8 0.4 - - - -
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Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLN* 3.1 14.8 + - - +
247A THR* 1.3 97.5 + - - +
249A LYS* 1.3 72.0 + - - +
250A ASN* 2.8 21.0 + - + +
289C PHE* 5.1 0.7 + - - -
290C THR* 3.0 14.0 + - - +
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ARG* 5.9 0.9 - - - +
245A PHE* 2.8 40.7 + - + +
246A LEU 4.3 5.1 + - - +
247A THR 3.8 1.0 - - - -
248A ASP* 1.3 75.9 - - - +
250A ASN* 1.3 56.3 + - - +
287A GLU* 3.4 47.5 + - - +
288A LYS 5.3 0.4 + - - -
289A PHE* 4.8 7.9 - - - -
249C LYS* 6.1 1.0 - - - +
287C GLU 4.6 6.9 + - - -
288C LYS* 3.0 36.0 + - + +
289C PHE* 3.0 9.2 - - + -
290C THR 2.8 18.9 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il